Kallisto produced slightly fewer alignments than HISAT2 (third bar, Fig. 1A). While Kallisto was expected to be more accurate than the mixed-genome HISAT2 method, the average percent error was 11.2%, compared with only 1.7% for HISAT2-mixed (Fig. 1B). The accuracy, however, was substantially lower than other alignment methods (Fig. 1C), causing us to abandon this approach.
